wwPDB Agreement
AGREEMENT
between
RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS (RCSB),
Piscataway New Jersey,
Rockville Maryland, and La Jolla California
and
MACROMOLECULAR STRUCTURE DATABASE (MSD), Hinxton United Kingdom
and
PROTEIN DATA BANK JAPAN, Osaka Japan
to form the
Worldwide Protein Data Bank (wwPDB)
Effective DateJuly 1, 2003
By signing this agreement, all members agree to accept the terms contained within.
AGREEMENT TO ESTABLISH THE WORLDWIDE PDB (wwPDB)
1.
Rationale
The Protein Data Bank (PDB) is a worldwide resource. At present, data
are deposited and processed by three groups: the PDB managed by the Research
Collaboratory for Structural Bioinformatics (RCSB), the Macromolecular
Structure Database (MSD) group at the European Bioinformatics Institute (EBI)
and the Protein Data Bank Japan (PDBj) group at the Institute for Protein Research
in Osaka University. All processed data are sent to the RCSB who oversee the process and distribute the
data worldwide.
It is essential for the progress of global science that the PDB data is maintained as a single archive of PDB data
and is kept freely and publicly available. The three groups are fully committed
to this principle. They also acknowledge the importance of global equality in
the ability to deposit and access data and the need to have true international
involvement and collaboration in maintaining the PDB.
The Worldwide Protein Data Bank (wwPDB) has been created to provide an
organizational structure whose purpose is to uphold these principles.
2.
Definition of membership in wwPDB
The founding members of the wwPDB are the PDB managed by the
Research Collaboratory for Structural Bioinformatics (RCSB), the Macromolecular
Structure Database (MSD) group at the European Bioinformatics Institute (EBI)
and the Protein Data Bank Japan (PDBj) group at the Institute for Protein Research
in Osaka University. All three organizations serve as deposition,
data processing and distribution sites.
Proposals for new members would be reviewed by the current membership starting two years
after the official establishment of wwPDB.
Questions about adherence to the guidelines set forth in Section 4 will be discussed at the yearly meetings of
wwPDB as described in section 6.5. Serious violations by a member will be considered by the
wwPDB as the basis for withdrawal of that site from membership.
3.
Definition of terms
3.1
The PDB archive consists of two sets of flat files:
3.2
The PDB exchange dictionary describes the
syntax and semantics of PDB data that are processed and exchanged. It is designed to provide consistency of
data that are processed by different people in different organizations. The definitive exchange dictionary is kept at
http://mmcif.pdb.org.
The term 'PDB archive' does not refer to the web sites,
browsers and database query engines that will continue to be developed by the
various sites.
Other data formats and delivery methods may be included in the PDB archive in the
future after full discussion and agreement among members. New formats must follow the naming and
description conventions of the PDB exchange dictionary.
Software is not part of the wwPDB.
4.
Guideline and responsibilities of the members of wwPDB
4.1
The members agree to act as distribution sites of the PDB
archive as defined in section 3.1 with identical mirror contents and
subdirectory structure.
4.2
One of the members, the
'archive
keeper' (see section 5.1) will control the central repository of the PDB archive. The
archive keeper
will have sole write access to the PDB ftp archive and control over the directory structure within the following guidelines:
4.2.1
The
archive keeper will coordinate the distribution of PDB identifiers
(currently the 4 letter codes) to all deposition sites. The use of identifiers by members of the
wwPDB resembling PDB 4-letter codes for other purposes is prohibited. The
four-letter code consists of a number (0-9) followed by 3 letters or numbers. Members
of the scientific community will be informed of this guideline and asked to conform.
4.2.2
Archival files in the PDB archive are distributed with
the reserved conventional names, in the form pdb<
entry_id>.ent where <
entry_id>
is a PDB 4-letter code,
e.g. pdb1abc.ent, for PDB format entries; r<
entry_id>sf.ent,
e.g. r1abcsf.ent for X-ray experimental data; <
entry_id>.mr,
e.g. 1abc.mr for NMR
experimental/constraints, <
entry_id>.cif,
e.g. 1abc.cif for mmCIF format entries; and
<
entry_id>.xml
e.g. 1abc.xml for canonical XML format entries. These file name
conventions are to identify archival PDB entries and should not be used for
other purposes.
4.3
The
'archive keeper'
has sole write access to the PDB exchange dictionary. All changes or
modifications of the PDB exchange dictionary will be agreed upon by the members
and will be reflected in the version number of the dictionary. The legacy PDB
format will not be modified unless there is a compelling reason to do so. If
that occurs the nature of the change will have to be agreed upon by all members
of
wwPDB and with 90 days notice to the community.
4.4
All members of
wwPDB will
keep all format documentation publicly available.
4.5
All members of
wwPDB
agree to the following guidelines for the redistribution of PDB files:
4.5.1
Data files containing PDB content
may incorporate the PDB 4-letter entry name
(e.g. 1ABC) in standard PDB records only if they are exactly the same as what
is residing in the PDB archive. This does not prevent databases from
including PDB entry_id's as cross-references where it is clear that they refer
to the PDB archive. PDB records refer to the standard PDB format.
4.5.2
The distribution of modified
PDB format data including the records: HEADER,
CAVEAT, REVDAT, SPRSDE, DBREF, SEQADV, and MODRES are not allowed.
4.5.3
The distribution of modified
PDB data in mmCIF format including categories in the dictionary category groups
DATABASE and AUDIT is prohibited.
4.5.4
The data dictionary for
canonical XML (i.e. the XML schema currently
http://pdbml.pdb.org/schema/pdbx.xsd) will be electronically
translated from the PDB exchange dictionary. Changes in the schema will automatically track changes in the exchange
dictionary. In addition to the canonical XML representation, XML data may also be delivered in a content consistent
form in which the coordinate records are presented as single record rather than
in the fully marked-up canonical form. The schema with abbreviated coordinate
records is currently at
http://pdbml.pdb.org/schema/pdbx-ext.xsd.
XML data files with abbreviated coordinate records will be identified as <
entry_id>-alt.xml, e.g. 1abc-alt.xml.
4.6
wwPDB members are encouraged to develop their own web sites and
views of the data. They may create full or partial mirrors of their sites. These mirrors must, however, adhere to the guidelines set forth in this
document.
5.
Initial status of wwPDB
5.1
The founding members of
wwPDB agree that the RCSB will act as
the
archive keeper as defined in
section 4.
5.2
If any member becomes unable to fulfill its
agreed role as described in this document, then a new agreement must be
reached. This will be done at the annual wwPDB meeting (section 6.5).
5.3
All members of the wwPDB will make every
attempt to adhere immediately to the guidelines that have been laid out in
section 4 of this agreement. Any current practice that is in violation of the
guidelines will be eliminated no later than six months from the signing of this
document.
6.
Establishment and operation of the wwPDB
6.1
Each member organization of
wwPDB
agrees to the terms set forth in this document as attested to
by their signature.
6.2
A new web site for
wwPDB
will be created by the archive keeper. This site will contain two headings: the definition and scope of the
wwPDB;
and pointers to the three sites. All members of the wwPDB will agree upon the contents of this site.
6.3
Any products created by
each of the sites must be under the heading of that site logo. Each site will
include a mission statement that describes the scope of their site and the
search functions that they are providing.
6.4
An Advisory Board will be
constituted whose role will be to review policy issues and adherence to the
guidelines of the
wwPDB. It will also serve as a forum for dispute
resolution. Each member of wwPDB will appoint two members to the
Advisory Board.
wwPDB will ask the International Union of Crystallography (IUCr) and the International Council
on Magnetic Resonance in Biological Systems (ICMRBS) each to appoint one
representative to the Advisory Board. The
wwPDB members may seek advice from their own oversight committees,
advisory boards and funding agencies as to the best representation of their site.
6.5
The
wwPDB will have a yearly meeting at a site determined by the
membership. Alternation of meeting sites is strongly encouraged. The meeting
will be attended by two representatives of each member of
wwPDB and members of the Advisory Board. The funding of the meeting
will be shared equitably among the three founding members of wwPDB. Prior to
each annual meeting the members of
wwPDB
will agree upon the plans for sharing expenses and who will be invited as
observers of the meeting.
6.6
The initial term of this agreement will,
assuming no review, be 10 years. After 5 years any partner may request review
of the agreement and production of a "renewal agreement". If unreviewed at 9
years, the agreement shall in any case be reviewed and a renewal agreement
produced. A 'renewal agreement' will come into force at the end of this
agreement or one year after the finalization of its text - which ever is
earlier. However, if all partners agree, a renewal agreement may come into
force earlier, at any point after its finalization.